Secret of NIMH 3
by AruaPearl44
Summary: Ash and the gang get preserve by Dr. Valentine and are now stuck in the world of NIMH. Ash turns evil, the rest of the human gang are Pokemon, and Pikachu is a NIMH mouse and escape. Can Thorn valley save the gang? Or will the worlds be doom?
1. The madness Begins

The Madness Begins

* * *

A long time ago there was a secret sacristy of science, it was called NIMH. The scientists expatriated on mice and rats. Somehow the rats became intelligent and were able to read. The rats except would have been hopeless with out Jonathan, unfroculently he didn't make it. The rats of NIMH now live in a secluded place called Throne Vally. There was an old owl that predicted that Jonathan's son, Timmy, would save the valley from the evil of NIMH. He did. The scientists were all haled to jail for life, never seeing the light of day again, and never being NIMH to the whole world. But the technological at NIMH is still there, waiting for something to prove it's work.

* * *

Ash Ketchem a dim child that wants to be the worlds greatest Pokemon Master. Unforgivably he has dark secrets, he and his friends that were there or he only knows, that stop him or villains to defeat.

Ash is travailing with his best friend and partner Pikachu; Brock, a breeder; Dawn, a newbie coordinator; and Dawn's partner Piplup. They traveled around collecting badges and ribbons to enter the Sinnoh league and the Sinnoh Grand Festival.

* * *

On their way to Sunnyshore City, for Ash's next badge and Dawn's next contest, our heroes were walking along until. "Hello, I'm doctor Valentine. And I would like you to come with me to a wonderful place." The white hair doctor said. "Nah, we're on our way to the gym."Ash said. "And onto my next contest." Dawn said. "Well if you help me I'll make your wildest dreams come true." Dr. Valentine said. "Really." Ash questioned what the doctor said. (And you should not listen to him, he's mad.) "Oh really." The doctor said. "Now come with me." "Okay." The gang agree.

* * *

After a plan ride to the place, the gang noticed it was (still) brunt up. "What happened here?" Brock asked.

"Well one of my experiments went hay wire on me and exploded." The bad doctor said. (He doesn't remember because of Timmy's brother going nuts and use one of his machines to turn his mind into a dog's.) Pikachu didn't like the place at all. (Well you Pikachu and every mouse in Thorn valley.) They went inside the hell hole. While they walked in Ash read on the side.

_National_

_Investment in_

_Mental _

_Health._

"NIMH." Ash said.

* * *

(The next day.)

"Man those beds hurt." Ash complained as he stretched his back. They were in the main lab. "So what do we do?" He asked the doctor, who was there.

The doctor stared at the gang then said. "You two go check the labels in the second floor lab. Boy you stay here and clean." He gave Ash a broom and pencils to Dawn and Brock.

* * *

(Second floor.)

"Man this is hard." Dawn said while looking at the beacons. She looked around. "What did they do here?" She asked nervously. Then Brock dropped a container. The fluid spilled over the floor and dissolved it."We better be careful this stuff is dangerous." Brock said. "Dawn why did we agree to this." "Because the doctor said he'll make our dreams come true." "Are you sure? We could get killed before we are able to achieve our dreams, the doctor could mutate us and do something horrible to the Pokemon, or he was lieing about helping us so we can do his dirty work." Dawn was shocked by the last part. "Your right Brock, lets get Ash and get out of here."

They and Dawn's Piplup climbed down the stairs to see Dr. Valentine standing on the bottom step. "Good to see you." The doctor said. "Don't worry about your friend I haven't seen him after the order." The gang sighed. "Dr. Valentine we want out now." The gang said in union. "Well then, you won't go now." The doctor said. "I don't care what you say, I just want to get out of here with my friends unchanged and never come back." Dawn said. "Well if you made the wrong chose for being rude when you said you want my help then you change your mind." Valentine said. "Well if I guest you'll be my new projects."

"Wahh!!" The gang said. "Piplup!!" Piplup screamed. "Pika!!" Pikachu yelled.

* * *

(With Ash. Warning: Bad things will happen next.)

"It's not that bad like the beds." Ash said. He was sweeping in the Doctor's room. "Huh." He looked on the table to see a weird helmet. Ash read the description on the helmet. _Makes dumb animals smart. Warning! Don't use it too much._ Ash took off his hat and put it on the table and put the helmet on his head. Pikachu was with Dawn and Brock so it couldn't stop Ash. "Well they always said I was dumb and acted like an animal. Maybe this thing can prove them wrong." He said. He turned the machine on. Huge amount of electricity went through his head. It increased his IQ up a bit. (This brings bad news to everyone everywhere.)

He continued to sweep the floor while the helmet was done it's thing. "Pika!!" Pikachu screamed. Ash turned off the machine and got it off while reaching for his hat, while dropping the broom. When he was done he went where the sound came from. Nobody was there. "I must be hearing things. I've probably learned something by now." Ash said. Ash you couldn't be more right.

* * *

(The next day.)

In the bed room Ash looked around and nobody was there. "Where is everybody?" He asked. "They weren't faithful enough to science so they went back on their journey." The Doctor lied. "Oh and what's your name, I have something for you to throw away after you get dress." "Yes sir." Ash said. 'Weird I'm not usually this obedient. I guess I'm smarter but I don't feel smarter.' Ash got his stuff on but while he got his vest on he notice it was more snugged than usually. 'Am I growing?' Ash thought.

* * *

Ash asked what was the thing he was to trow away. The Doctor pointed to the helmet thing. "What's wrong with it?" He asked. "Well when I used it on one of my rats, it got so smart that it was able to use that same machine to turn my mind into a dog's." He said. "It's too powerful to use." Ash didn't laughed even though it was very funny. When the doctor left Ash bong it to his room. "Even though he said it's dangerous I feel more delighted when I use it." Ash said while caring the machine. When he got it to his room he plugged it in, took off his hat, put the helmet on his head, then turned the thing on. After an hour of the electricity Ash turned it off, feeling pleased with himself.

"Dawn, Brock and Pikachu won't leave me all alone, would they?" He asked himself as he lide on his bed. He put the machine under it. The doctor came in and dropped a book on Ash. "You will be my new assistant and help me with stuff around the lab. You will write what you learned in this book as a journal." Dr. Valintin said.

* * *

**Me: Uh oh. This helmet thing is going to be bad news. wounder what happened to Dawn, Brock, and the Pokemon.**

**Ash:Hey why are you doing this to me?**

**Me:Because I like weird stuff and I was bored.**

**Ash fell backwards, anime style.**

**Me:I'm tiring a new style of writing these parts.  
**

**Me:Until next time.**

**Me:Ash do you have something to say.**

**Ash:A right. AuraPearl44 owns nothing, everything belongs to the original owners. Hey why are we doing this?**

**ME:Because I don't want to be sewed. And if I did own Pokemon I would make Ash and Dawn a couple, bring back the king of Pokelantic, tell who is Ash's and Dawn's father already and do some weird stuff.  
**

**Ash:Why do you want the King back?**

**Ash didn't like it when he was posse.**

**Me:Only for a few episodes then I would get ride of him. (Not really. But Ash doesn't need to know.)**

**Ash sighs.**

**Me and Ash:AuraPearl44_May the Aura be with you_Peace.**


	2. Journal Entries

Ch. 2 Journal Entries

* * *

Day 1 after getting journal.

The doctor showed me around the place but there was one place I haven't seen yet. The animal contaminant room. He said that I need to wait until he fully trusts me. But I didn't do anything wrong.

* * *

Day2

Things here are pretty boring because Dr. Valentine didn't tell me what to do, so I just used that cool machine I fond all day. I'm feeling so much smarter now, I can understand what Misty meant to said from all those years ago.

* * *

Day 3

My clothes don't fit me anymore. I guess I'm finally growing. Now nobody will call me baby and mistake me for their child.

The doctor got me new clothes that are like my clothes but bigger.

Other than that nothing happened. I didn't even touch the machine today.

* * *

Day 6

I finnaly learn something from Dr. Valentine. He explains the threnody of the universes in this world. It was so boring. I still think that this world is not my world for one there aren't any Pokemon when I look out the window.

* * *

Day 8

The doctor showed me that room, I can't believe it. He has Dawn's Piplup and Brock's Crogunck locked up in there and they are miserable along with their Pokeballs and mine. Also there's this mouse that reminds me of Pikachu there too. I think he's going to mutant them. I have to stop him but how.

* * *

Day 9

I rerouted the machine he gave me to fix and turn his brain to mush. He's now dead and I don't feel bad about it. I wounder why.

* * *

Day 14

I think I'm losing it. _Soon I will rule the world. _What did I just write. I must be losing it.

Oh I wish Dawn and Pikachu were here.


	3. Run Away

Ch. 3 Run Away

Day 15.

Ash just woke up from a weird nightmare. But he didn't remember it, so he ignore it.

Ash got his clothes on then looked at the machine. He put it on and started it up. After a few minutes passed he shut it off and took it off. Then he went outside.

He took a deep breath then exhaled black aura. Then smiled an evil smile. "Well I better go check on the creatures." He said.

Ash walked in the experiment room and looked at the unhappy Piplup and Crogunk. They looked up and saw him. They were very happy to see their old friend again. "Piplup. Piplup, pip lup lup! Pip piip pup?" The Piplup asked. (Ash. Ash, its you! Where that crazy doctor?) Ash noticed it was a girl and asked about the doctor. "Don't worry." He said cheerfully. "I kill him." Then Piplup and Crogunk where shock and scared. Did he say he killed him. Then Piplup fainted. "Cro, gunk gunk. Crogunk cro?" (Ash, you did that. What happen to you?) The Crogunk asked.

"I was modified by a wonderful machine. Now lets wake up the mouse. I heard from Dr. Valentine, before I kill him, that that mouse hasn't woke up even once." Ash said then he went to the mouse's cage. Ash grabbed it gently and showed it to the Pokemon. It looked like the older version of Timmy from Secret of NIMH 2 but with lighter fur and two brown spots on his back. "Come on now and wake up." Ash said. Piplup and the mouse woke up to see Ash charming face. "Pi? Pika pii chu?" The mouse said. (Huh? What happened to me?) "Chu?" (Who are you?)

Small tears were coming out of Ash's face. "I'm Ash. And you sound like my old pal, Pikachu." He said. "Piplup. pip lup pip lup." The Piplup said. (Run away. He's really crazy now.) "Pika pii chu?" (But where should I go?) The mouse said. "Pip lup pip lup pip, piplup piplup." The penguin Pokemon said. (South by south by south, a police station should be there.) Then the mouse ran away. Ash did nothing to stop it. "Now it's time to train my aura I'm going to have a busy afternoon." Ash said.

Piplup and Crogunk looked at Ash funny. Why didn't he shut Dawn/Piplup up? What is this machine he was talking about? And what is he going to do next? That was on their minds.

With Ash.

He was outside, training his aura when the real Ash came up. "Why didn't I let them go? That guy is dead now so why am I still keeping them caged up." Ash questioned. His head began to hurt. :Because I need to show the world to never a banded me.: A voice said. "Who are you?" Ash asked. :I'm you. Or should I say, I'm the better you.: The voice said. "What are you going to do?" Ash asked. :I'm going to destroy Thorn Valley then rule the rest of the world.: The voice said. :You could have stopped me by never putting that helmet on but we needed the upgrade. Thanks.: "Wait." Ash said then Ash felt pain like he did when he was posse by the King of Pokelantic.

Then the Ash from ealier was back. "Now that that Piplup had gave the directions to Thorn Valley I just have to wait til he gets there. Then I'll unlease my master plan. But first I need to build up an army." Ash said. "Oh and lock up my old self so he won't interfer like he did now." Then Ash walked to the lab.

**Ash: What did you do to me?**

**Aura: I weird so I did something weird case close.**

**Ash almost hit me. But I douged.**

**Aura: Man, you need anger manigment. Anyways it not real. I just make stuff up like this.**

**Ash sigh.**

**Aura:The next chapter will involve the rats or mice of NIMH. Ash it's your turn.  
**

**Ash:AuraPearl44 doesn't own anything.**

**Aura and Ash:AuraPearl44_May the Aura be with you_Peace.  
**


	4. Hiching a Ride

Hitching a Ride

The mouse from the last chapter was running south by south by south when he was totally lost in a wood. "Hello, can anybody help me?" He called out. "I can." A female voice said. Then a mouse wearing a pink sweater walked up to him. "I'm Martha. I live in a place called Thorn Valley. I heard you call and wanted to know what's your problem?" She asked. "I'm looking for a police station. A penguin and a frog are trapped in a place called NIMH. I escaped." The mouse said.

Martha was afraid. "I need to take you the console." She said. Then they ran off to a small village. They entered a church like building. After comforting what the mouse said, the leader asked. "How are you?" "I'm Tim." The mouse said. "And if what your saying is true then how is the place running now?" A buff mouse asked. "A black hair guy name Ash controls the place. He said he killed a guy name Valentine." Tim said. "That man must be more insane than the Dr." A mouse said. "Your right. But it's too dangerous to go." The leader said. "You will stay with Martha while we come up with a plan." The leader said. Then the two mice left.

(That night.)

"I don't think they're going to rescue my friends." Tim said. "Yay. Those guys are all old. Why don't we go and rescue them." Martha said. "How where stuck in this room." Tim said. "I have a plan." She said.

(Outside on a bridge.)

"Alert. It seems Tim and Martha are running away." The buff mouse said. "They seem to be using the river. Don't let them escape." "Yes Captain Capper." The guards said. Then one of them spotted something. "There they are." Guard 1 said. Then Captain Capper pulled their tails out of the water while saying. "Well it seems we have ourselves... bogeys." He said as he realized they were actually plunges with rope tails. Then a seat with tons of balloons flew up and out of Thorn Valley. "There they are." Guard 2 said. "They're too high to get to." The captain said. Then he went to the console.

(On the balloon.)

"Do you know how to fly this thing?" Tim asked. "Yes. From the ground." Martha said. "If we die I'm going to kill you." Tim said. "How do you do that when we're already dead?" She asked. Tim was at a lost of words. Then they rappelling fall a little. "What was that?" Tim asked. Martha looked up. "Birds." She said. Then a bird poked some more balloons. They fell some more. Then the seat was uneven and the left part fell. Tim grabbed the rest of the balloons. "Grab my hand." He said. And Martha did. Then more birds attacked the balloons.

After they popped the last balloon, Tim and Martha fell into the field below. Surprisingly they serviced. "I told you. If we die..." Tim said. "Don't worry. We're still alive." Martha said. Then the birds flew over there. They ran away to a hollow tree. "Boo! Stay away from here!" A load ominous voice said. Then the birds flew away. Then a caterpillar walked their way. "I'd thought I told you people to keep birds away from here." The caterpillar said. "I'm sorry." Martha said.

"Wait a minute, how do you know this guy?" Tim asked. "Tim this is Henry the third. He helped my dad take down NIMH a few years ago." Martha said. "Yeah and it was spooky." Henry said. "Uhm Henry we have to go back to NIMH. It seems it resurface." Martha said. "That's totally bad. I'll get Jaramy." Henry said. Then he went off.

"So who's Jaramy?" Tim asked. "A crow that help my grandma and my father." Martha said. Then a large crow. "Sorry Martha that I missed you but I was getting aquanaut with a very strange bird." Jaramy said. Then a Piplup slid down it's wing. "Hi I'm Piplup." The strange bird type said in a guy voice. Then it looked at Tim. They were about the same height. "You look like Pichachu." Piplup said. "What's a Pikachu?" Tim asked. "My friend but he wasn't able to escape like me." Piplup said.

"I met him weeks ago. He seemed pretty lost so I kind of adopted him." Jaramy said. "But I do regrade leaving my master and friends in NIMH." Piplup said. "You escaped from NIMH. Were you mutated in anyway." Martha asked. "No but I don't know about my friends. I left before that Dr. Valentine could notice me." Piplup said.

"Well you don't worry about Dr. Valentine cause he's dead." Tim said. "Great now I can save my friends." Piplup said. "But his apprentice killed him and took over the place." Tim continued. "So what's his name?" Piplup said. They looked at him. "How can I know how to defeat my new enemy if I don't even know his name. Shesh." Piplup said. "His name is Ash." Tim said.

Piplup was frozen in fear. "I know. He's a monster." Tim said. "No. It's just. Ash is my friend but why would he do such a thing." Piplup said. "What are you talking about?" Martha asked. "Well, Ash is the most kind hearten boy I know. And he would never kill someone. Are you sure its the same Ash?" Piplup asked. "He has squiggly marks under his eyes and he has messy black hair." Tim said. "That's the same guy. Why don't I go with you to find out what happen to him." Piplup said.

"Sure just don't slow us down." Martha said. "Okay." Piplup said. Then they climbed onto the crow. "Next stop, NIMH." Jaramy said. Then he lifted off to North, by north, by north.

**Piplup has arrived. What will happen next? Will they be able to save Ash? Stay tune.**

**AuraPear44_May the Aura be with you_Peace.  
**


	5. Rescue

Rescue

Tim, Martha, Jaramy, and Piplup flew all the way to NIMH then Jeramey landed. "That's all I can take you." Jeramey said. "Thanks. It was a big help." Tim said. Then they crawled through the gates and entered the building. "Man this place is creepier than I remember." Piplup said. Then they reached a mail shot. "My friends are on the second floor, we can use this shot to get there." Tim said. Then they climbed up it. Piplup had a little trouble since he's a bird but he manged to get to the second floor.

They reached a corner when they stopped. Suddenly huge rats matched down the hall ways. They were orange and had Lighting tails. "Those must be Raichus." Piplup said. "Their the biggest rats I've ever seen." Martha said. Then the Raichus left. The gang ran until they reached the room they were looking for. Suddenly they bumped into Captain Capper and some mice. "What are you doing here?" Martha asked. "Since the console are still arguing. We discided to help you." The Captain said. Then they entered the room. It was full of Pokemon from the trainers. They looked the same as they should be. "Help." The Mamoswine asked in a huge cage where all the lager Pokemon too big for the smaller cages.

Then they reached the Piplup and Crogunk. Next to them was another Crogunk. "All right we're here to save you." Martha said. "Thanks." Dawn said. Then Piplup and Dawn looked at each other. "Dawn?" Piplup asked. "Piplup?" Dawn asked. Then they cried. "I thought I never see you again." Piplup cried. "Me too." Dawn said. Then Martha opened the cage. "So how did you turn into a Piplup?" Piplup asked. "The doctor mutated us and put us in theses cells." Dawn said. "Wait. You were something else." The captain said. "Yeah human." Brock said. "Wow that's weird." Tim said. "And you use to be a Pikachu." Brock said to Tim. "Wow that's super weird." Tim said. "I knew you looked familiar." Piplup said. "Alright. Now we have to rescue the others." The Captain said.

Then the door opened and revealed a knockout gas. Everything was knocked out.

("_Words" =_ Pokemon/animals. "Words"= Human.)(Ash can understand them.)

Tim woke up in the arms of a Raichu. Dawn and Martha were trapped too. The others were in cages. "Ah if it isn't the hero." A voice said. Then Ash appeared. He got taller and his hair was wilder. His smile looked wicked and crooked. _"Ash. Snap out of it."_ Piplup said. Ash chuckled. "Why should a traitor be warred about me?" Ash asked. This confused them. "Now I shall tech the world to never ignore me again." This scared them. _"Ash we never abandoned you."_ Dawn said. "Shut up you stupid bird." Ash yelled. Then he turned to Tim. "You thought you save your friends but it is a ruse. I only let you go so I can get directions to Thorn Valley. Once it's gone I'll go to real cities. One test would do. And then the world would fear me. And I would never be abandoned again."

_"That's crazy."_ Tim said. "Yes but you might not mind once you're like me." Ash said. "Bring it out." He yelled. Then some Riachus bring out a machine. It was smaller than Ash's. _"No it can't be." _Martha said. Tim looked at her. _"What is it?" _He asked. _"That machine that turned my uncle into a mad mouse. My father was able to free though." _Martha said. _"That must have been the machine he was talking about." _Brock said. "Bravo you figured it out. But you are too late once I have this connected to you hero, then you'll be just like me." Ash said._ "NO!" _Tim said.

Ash got angry. "Strap him to the machine." Ash yells. Once it was done Ash was about to throw the switch when the Ash we know came back. "No. No! I won't let you do this." Ash yelled to himself. "I thought I got rid of you. And yes you will." The other Ash said. "No." "Yes." "No." "Yes." They fought.

_"Now while he's confused." _Martha said. Then Piplup and Dawn used Peak on their guards. Then released Tim and Martha. Ash was still fighting with himself when that happened. _"Thanks guys." _Tim said. _"No sweat." _Dawn said. _"Now what do we do?" _Piplup asked. _"Ash is still in there we just have to free him." _Dawn said._ "Say you were a Pikachu before." _Martha said. _"Yeah." _Tim said. _"Well if you can shock him while he's on your friend then the crazy part might go away." _Martha said. _"Yeah but we don't know if he can still collect electricity." _Piplup said.

_"We have to try." _Tim said. Then he started to concentrate. Ash was still fighting with him self with no winner. Suddenly Tim was able to zap him. _"We did it." _Tim said. "Yes you did." Ash said all creepy like. _"Come on Ash lets go." _Piplup said. Then Ash started to strangle him._ "Ash!" _Dawn and Brock yelled. "Thanks for getting rid of that pest. I guess his will didn't want to die yet." Ash said. Tim started to charge up but Martha stopped him. _"No you'll shock Piplup." _Martha said. _"What do we do?" _Tim asked. "Nothing. There is nothing you can do." Ash said. Suddenly he felt pain, like a needle. And he collapsed. _"What happened?" _Brock asked. Then a police woman with blue hair came in. "You are under arrest." Jenny said. _"It's officer Jenny!" _Dawn and Brock yelled, mostly Brock.

"Just as my inside man said an experimental lab. Now to hail... Wait somethings wrong?" Jenny said. Then she checked his plus. "He's dead." Jenny said. This sadden the creatures. "But how that needle was only to know him unconscious." Jenny said. Then she called the hospitable.

(During that time.)

Ash was in a space. "What happened?" Ash asked. "Where am I?" Then fire was ever where. Ash covered his mouth. Then he saw himself in the flames. "Am I dead?" Ash asked. He waked over to the other one. "Dawn, Pikachu, Brock?" Ash asked. The other one woke up. This scared the first Ash. "What happened?" He asked. He looked around and saw the fire and the other self. "What happened to the lab?" He asked. Then he coughed. "Don't breath it in." Ash said. Then he looked around and saw they were on a platform that moved up and down. The first Ash throw a rock at a button and the elevator thing when up.

"What do we do? We'll crash into the ceiling." The second Ash asked. Then they fond a mental box big enough to fit both of them. Ash pushed him to the box and crawled inside. He closed the lid and they flew into the sky. "Why did you help me?" The second one asked. "I tried to seal you away." "Well. If I believe enough then I can do anything. Besides I know from experience that you're not that bad inside." The first Ash said.

"Thanks. That's the first time someone was nice to me." He said. Then he started to disappear. "What's happening to you?" Ash asked his doubler. "It seems my time is up. I had a great time with you. Maybe you will met someone that will make you whole. I know I have. Good bye..." He said. Then everything was white.

(Now)

Ash woke up to see Dawn, Brock, Piplup and two mice. "What happened?" Ash asked as he looked around. "You were in a coma but we were able to save you." Dawn said. "How long was I out?" Ash asked. "A few days." Brock said. "But we were able to get back to normal by then." Dawn said. "Yeah. Jenny came when she heard someone reopened that nut place." Brock said. "She knocked you out and fond out what happened."

"So all those things were true?" Ash asked. "Yeah. But the doctors were able to get rid of that other you." Dawn said. Ash looked sad. "Ash he was going to anything to rule the world. You should be happy Jenny saved you before you got too deep." Dawn said.

Ash nodded. "So these two are together." Ash said. "Yeah. Pikachu like being Tim so much that he refused to go back to his old life." Brock said.

"So that means our team's up." Ash said. This confused them. "Pikachu was my only companion when I was alone when he was gone I fell into temptation. I can't go back." Ash said. Then they looked at each other. "What do I do?" Ash asked. He started to cry. Then he felt a hand on his back. "We're with you." Dawn said. Ash smiled. "And you promise you won't leave." Ash said. "Promise." Dawn said.

(Later.)

They were outside the hospital. Jenny was there. "Are you going to send me to jail?" Ash asked. "No. I felt sorry I hurt you so I came to apologize." She said. Then she quickly left. "So this is the end of the road for you and I?" Ash said to Tim. _"Guess so." _Tim said.

"I hope we see each other someday." Ash said. _"Me too." _tim said. "Bye." _"Bye." _Then they went their sepret ways.

**A sad ending. And to tell you this is the end. And I won't make a secule.**

**Hoped you liked it. **

**AuraPearl44_May the Aura be with you_Peace.  
**


End file.
